This story takes place between Boom Town and Bad Wolf. It also includes references (aka, SPOILERS) to the Ninth Doctor novels "Winner Takes All" and "The Deviant Strain", in case anyone is curious or wants to read them.
"Okay, Doctor, just another minute." Jack said as he typed a few more commands into the console and adjusted the hololens.
The Doctor stood with one hand in his pocket, looking down at the metal grating that made up the floor of the console room. Through the grating he could see various boxes and trunks where he kept his archives. Directly below his feet was a trunk marked with a "D". Inside he knew he could find early schematics of K-9, a Dalek's eyestalk, and probably a model of a double-helix, among other things.
The sound of the hologram camera sputtering to life broke into his thoughts, followed a moment later by Jack's voice. "Recording in three, two, one."
The Doctor took a deep breath, and looked up at the camera. "This is Emergency Programme One. Rose, now listen. This is important. If this message is activated, then it can only mean one thing: we must be in danger. And I mean fatal. I'm dead, or about to die any second with no chance of escape, and that's okay. I hope it's a good death. But I promised to look after you, and that's what I'm doing. The TARDIS is taking you home."
He paused, anticipating Rose's response, then continued. "And I bet you're fussing and moaning now. Typical." He emphasized the word with a jerky nod of his head.
"But just hold on and listen for a bit more. The TARDIS can never return for me. Emergency Programme One means I'm facing an enemy that should never get their hands on this machine. So this is what you should do: let the TARDIS die. Just let this old box gather dust. No one can open it, no one will even notice it. Let it become a strange little thing standing on a street corner. And over the years the world will move on and the box will be buried." That was hard to say. The Doctor couldn't imagine ever allowing that to happen. But there was no protesting or frightened chime at the edge of his mind. She accepted that fact. Now the Doctor had something even harder to say.
"And if you want to remember me, then you can do one thing. That's all. One thing." He paused again, and made a calculated guess. He turned his head to the left and smiled a little. "Have a good life. Do that for me, Rose. Have a fantastic life."
The Doctor fell silent and heard Jack turn off the hologram camera. He could imagine Rose standing right there, right where he was looking, if this message were ever activated. He had one more thing to add, something he was too afraid to say to the camera. Nevertheless, he hoped some echo of it would survive, and Rose would somehow know just how much she meant to him.
"I love you." He murmured.
"You say something, Doctor?" Jack looked up from the screen where he was saving the recording and setting it to play should any of a dozen different parameters he and the Doctor had discussed were ever met. The Doctor was still standing and staring at the spot where Rose would see it if it were ever activated.
"Nope. Just clearing my throat." The Doctor lied as best he could.
Evidently, it was not a convincing lie, because Jack left the console and moved to stand beside the Doctor.
"We're doing the best we can for her." Jack said, putting one hand on the Doctor's shoulder. The Doctor only nodded, thinking of the all too frequent close calls. Being stolen by Quevvils and forced to be a player in their war games while he controlled her every move, just trying to keep her alive. Being chased through decaying nuclear submarines to escape the clutches of a Russian police woman. Ordinarily not too much of a challenge, except that she was being kept alive and strong well past her time by using a crashed alien ship to suck the energy out of anyone she could. And most recently, nearly being the victim of another Slitheen plot. For a few terrible moments, he was faced with a single choice; he could save the world or save Rose.
Who was he to choose a single person over an entire species? Even if that person was a small pink and yellow girl who held his hand and had a special smile just for him? Especially if, when the situation was explained, she was willing to make the choice for him? And even after explaining what her choice meant, she still didn't choose herself?
Thankfully, it had all come through in the end, and he had been able to save all parties involved. He'd even had a hand in helping Margaret receive a second chance at life. When the TARDIS had asked him if it was a good idea, the Doctor had vouched for the criminal Slitheen. But he had finally pushed his luck too narrowly when it came to his Rose. She would not die because of him. Not if he could at all help it. He wouldn't risk her life like that again.
Knowing she would be safe made him feel like he could face anything. She was his world now.